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Nuclear Receptors and Their Classifications

Nuclear Receptors

Nuclear receptors are a family of ligand-regulated transcription factors with important physiological functions. These receptors are located in the cytoplasm or the nucleus of the cell. Nuclear receptors are classified as transcription factors due to their ability to bind directly to DNA and regulate the expression of adjacent genes. They are a class of proteins responsible for sensing steroids, hormones, vitamins, and certain other molecules. By modulating the expression of specific genes involved in various cellular functions, these transcription factors mediate the effects of small molecule drugs, hormones, and other xenobiotics. They play an important role in embryonic development and adult homeostasis while influencing a wide variety of functions including fatty acid metabolism and detoxification of foreign substances.


Nuclear Receptor Families

Nuclear receptors are classified according to mechanism or amino acid sequence homology. In 1999, the Nuclear Receptors Nomenclature Committee created organizational nomenclature based on nuclear receptor’s phylogenetic tree. The committee decided on the form structure NRxyz in which x is the sub-family, y is the group, and z is the gene. The systematic nomenclature of nuclear receptors divides the family into NR1, NR2, NR3, NR4, NR5, NR6, and NR0. However, many nuclear receptors are known by their trivial names based on their first discovered ligands, such as estrogen receptor or thyroid hormone receptor.

Structure of Nuclear Receptors

A nuclear receptor’s structure can be broken down into four domains.

  • The N-Terminal domain, or A/B domain, is the first domain, known as the hypervariable or regulatory domain. This is an incredibly disordered domain, not compliant to structural analysis.
  • The DNA-binding domain (DBD), or C domain, represents the most conserved domain. The DBD contains two subdomains that each consist of four cysteine residues that organize a zinc ion to create the canonical DNA‐binding zinc finger motif.
  • The flexible hinge region, or D domain, contains the carboxy-terminal extension of the DBD and acts as a link between the DBD and ligand binding domain.
  • The ligand binding domain (LBD), or E/F Domain, is a complex domain that not only binds to ligands but also interacts directly with co-regulator proteins. This variability across nuclear receptors at the ligand‐binding region allows nuclear receptors to identify a diverse group of ligands.

There are 48 human nuclear receptors, several of which do not have an identified natural ligand and are considered orphan receptors. All nuclear receptors have evolutionarily-conserved sequence similarity, especially within the DNA binding domain and the ligand binding domain. The exception is a small subfamily of receptors that does not contain a DNA-binding domain (SHP-1, DAX-1), but instead bind to other nuclear receptors.

Types of Nuclear Receptor Activity

Nuclear receptor ligands may cause considerably different effects including agonism, antagonism, and inverse agonism.

  • An agonist is a ligand that increases the activity of a receptor above its constitutive level.
  • An antagonist is a type of ligand that will block agonist-mediated responses by competing at the ligand binding domain of the receptor.
  • An inverse agonist binds to a constitutively active nuclear receptor and causes a dose-dependent decrease in transcriptional activity.

Classification of Nuclear Receptors

The system in which a given nuclear receptor participates can be defined in several ways such as sequence similarity, potential disease implication, or transcriptional networks. In terms of functional classification, nuclear receptors can be grouped by those that affect:

  • CNS, Circadian, and Basal Metabolism
  • Lipid Metabolism and Energy
  • Reproduction and Development, and
  • Xenobiotic and Bile Acid Metabolism.

Nuclear Receptors in Drug Discovery and Environmental Toxicology

In drug discovery, nuclear receptors are used to prospectively understand on- and off-target effects that small molecules may have. Drug profiling studies include testing a compound across various nuclear receptors to better understand the poly pharmacology of a drug candidate and its potential biological and toxicological effects.

Since the receptors interact with a variety of lipophilic ligands, they can also be used to examine chemicals in the environment (water, soil, food) as individual compounds or complex mixtures. The one-chemical-at-a-time approach has been applied for examination of environmental quality, leading to insufficient knowledge about health effects caused by exposure to mixtures of chemicals that have the same target. To circumvent this challenge, researchers can employ in vitro assays to analyze the exposure to and human health effects from chemical mixtures in environmental samples. The advantages of using in vitro assays are that an integrated effect is measured, taking combined mixture effects into account, and that in vitro assays can reduce complexity in identification of Chemicals of Emerging Concern (CECs).

Nuclear Receptor Reporter Assays

Cell-based nuclear receptor reporter assays are valuable for scientists seeking to understand the effects of potential therapeutic compounds, chemical compounds such as pesticides or industrial chemicals, and environmental contaminants. Cell-based reporter assays, such as those offered by INDIGO Biosciences, can provide information about a chemical’s effects, either activating or inhibiting, on specific nuclear receptors. To learn more about how INDIGO’s nuclear receptor reporter assays can be used in your research to save you time, contact us today!